This has been driving me nuts for months too, and today I figured out that when I press Command+F (in that order), the F key press doesn't register. However, if I flip the order by pressing F + Command, it works again. That seems to "reset" something so that I'm able to continue using Command+F for the rest of that session. I hope this helps!

You can do it like this:

System preferences -> Keyboard -> Shortcuts -> App Shortcuts

Click + And select Safari as Application.

Then enter the exact name of menu command (In your case: Find…) and enter your preferred hotkeys (Control + F on the screenshot)

I have had this exact problem for weeks, and it's been driving me crazy, but I've finally found a solution. I found this thread on the Apple Support Communities, where “stevendeluxe” says the following:

Problem fixed! I compared the system preferences for each user and found out that I had several languages activated in the language/region settings. So I deleted the language adding the option "list sort order". This option wasn't activated in my test account.

You have to try which language is the "bad one" on your system (In my case it was "german"...haha) and delete it. UPDATE: I've tried to re-add the deleted language and still safari works fine.

I did the same, went to “Language & Region” in OS X System Preferences (found in the Apple menu at the top left of the screen), and removed two languages I'd added as a lark (Swiss German and Klingon, to be precise), and after restarting the computer (which OS X requires if you remove the primary language), all my keyboard shortcuts work again. Joy and jubilation.

I hope this works for you, too.